Table 1.
SLE Risk Loci Surpassing the Genome-wide Significance Thresholda
| Chr | SNP | Locus | Allelesb |
European (3,562 Cases/3,491 Controls) |
African American (1,527 Cases/1,811 Controls) |
Asian (1,265 Cases/1,260 Controls) |
Meta |
Test of Heterogeneity |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| pGWA scanc | ORGWA scan (95% Cl) | pREP | ORREP (95% Cl) | pMETA-Euro | p | OR (95% Cl) | p | OR (95% Cl) | pMETA-ALLd | pQe | I2 | ||||
| 3 | rs1132200 | TMEM39A | G/A | 1.65 × 10−3 | 0.72 (0.59–0.88) | 2.37 × 10−4 | 0.83 (0.76–0.92) | 1.81 × 10−6 | 6.92 × 10−2 | 0.75 (0.56–1.02) | 1.66 × 10−3 | 0.73 (0.59–0.89) | 8.62 × 10−9 | 0.450 | 0.0% |
| 16 | rs11644034 | IRF8 | G/A | 2.29 × 10−3 | 0.66 (0.54–0.79) | 2.36 × 10−8 | 0.78 (0.71–0.85) | 2.08 × 10−10 | 5.10 × 10−1 | 0.95 (0.81–1.11) | 2.63 × 10−2 | 0.79 (0.65–0.97) | 2.72 × 10−9 | 0.016 | 61.5% |
| 16 | rs11648084 | IRF8 | G/A | 5.99 × 10−4 | 0.76 (0.65–0.89) | 9.35 × 10−7 | 0.83 (0.77–0.89) | 2.34 × 10−9 | 6.33 × 10−2 | 0.90 (0.81–1.01) | 7.52 × 10−1 | 1.02 (0.91–1.14) | 7.00 × 10−7 | 0.001 | 74.0% |
| 17 | rs9913957 | IKZF3 | A/G | 7.87 × 10−3 | 1.75 (1.27–2.41) | 5.14 × 10−4 | 1.38 (1.15–1.66) | 1.38 × 10−5 | 1.07 × 10−2 | 1.22 (1.05–1.41) | − | − | 1.39 × 10−8 | 0.105 | 45.1% |
| 17 | rs8076347 | IKZF3 | C/A | 3.07 × 10−3 | 1.93 (1.41–2.62) | 3.04 × 10−3 | 1.32 (1.10–1.58) | 4.75 × 10−5 | 2.19 × 10−3 | 1.20 (1.07–1.34) | − | − | 3.01 × 10−8 | 0.047 | 55.4% |
| 17 | rs8079075 | IKZF3 | A/G | 1.47 × 10−3 | 1.90 (1.39–2.59) | 5.08 × 10−4 | 1.39 (1.16–1.68) | 3.81 × 10−6 | 2.62 × 10−3 | 1.26 (1.08–1.46) | − | − | 4.83 × 10−9 | 0.201 | 31.3% |
| 17 | rs1453560 | ZPBP2 | A/C | 7.81 × 10−4 | 1.92 (1.41–2.61) | 6.42 × 10−4 | 1.37 (1.14–1.64) | 3.21 × 10−6 | 4.86 × 10−4 | 1.23 (1.09–1.37) | − | − | 3.48 × 10−10 | 0.097 | 46.4% |
The following abbreviations are used: Chr, chromosome; OR, odds ratio; GWA, genome-wide association; REP, replication; and CI, confidence interval.
a
Table S7 contains results for all populations evaluated within this study.
b
Major/minor alleles.
c
Result of GWA scan was previously reported in Graham et al.1
d
Data were combined for all racial groups genotyped within our study that passed quality control.
e
Cochran's Q test statistic.